My Little Ninjas: Masters of Harmony
by Spottedfrost7
Summary: Sensei Wu has been gone for months now, leaving the ninja to survive without his guidance. Trouble seems to be disappearing, however a new problem rocks thier world by taking them somewhere else. Can the ninjas take on this new challenge, or is this the end? Story way better then summary. It's a crossover but no one goes there so... yeah. Please read before you judge.
1. Chapter 1

**_Chapter One: Figures in my Eye_**

 **I know, I know. What are you doing Spottedfrost? You still have a thousand unfinished stories and you're starting a new one? Yeah, I am. I had to write this. Hopefully now that the app has a publish feature, I can finish more stories. I need to fix a lot, as my writing has gotten better. So bare with me until this is straightened out. Until then, have faith.**

 **Takes place between Season 7 and 8. Most definitely an AU, and is a crossover between Ninjago and MLP, but no one goes to the crossover section anyway.**

 **I don't own anything except the concept. P.S. Maybe review what you'd like to see, or what you think might happen. Sometimes it's you readers that give me ideas.**

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Lloyd sat on the floor, trying to meditate. It was something Sensei Wu had tried to teach him before… before _he_ left. _'I still can't believe he's gone. And they expect ME to lead.'_ The green ninja shook his head, and with it he tried to shake away his terrified emotions. "Empty your mind Lloyd. Let all negative thoughts and feelings slip away." Zane's robotic voice came from next to him. Since _he_ left, Zane had taken up on teaching him to meditate. It was his way of dealing with the pain.

They all dealt with it one way or another. Jay kept tinkering with small trinkets, occasionally helping Nya with her projects. Cole kept himself busy; working out, fixing things, cleaning, or even helping Kai and Nya's parents when they asked. _Kai_. The fiery ninja helped everyone else, taking a part time job to pay for groceries or for random parts Jay and Nya needed. He seemed normal, but if you looked into his eyes, you'd see the pain and guilt. ' _He still blames himself, even after we told him it wasn't his fault.'_

Lloyd sighed deeply, opening his eyes. "I can't do it Zane. My mind is just too full." His nindroid friend looked up at him, understanding painting his glowing eyes. "Perhaps we can try again later." Zane replied, standing up. "It is almost time for dinner. I will be in the kitchen if you need me." The nindroid made his way to the kitchen as Lloyd stood up. _'What are we going to do? Why did you leave us uncle?'_ The green ninja sighed, something he seemed to be doing a lot more of lately. He left the room and headed down the hall to where Cole's room was.

The door was ajar, allowing Lloyd to see that the black ninja was packing a backpack. Littered around the pack was a few water bottles and some snacks like trail mix. Oddly enough, there was a camera among the items. "What are doing Cole?" Lloyd asked, curious as to what his friend was doing. The ninja in question looked up, slightly startled that he hadn't noticed Lloyd. "I'm going for a run." Cole said, throwing an mp3 player into the pack. "What's the camera for?" Cole just shrugged. "To take pictures." That's all he offered, so Lloyd let it be.

"Where's Kai?" Cole asked as he tied his shoes. "He's gathering shopping lists again." The green ninja explained. "That time of month again?" It was more a statement then a question. Once a month, Kai would collect a list from everyone and head to the store. Then he'd return hours later with full shopping bags and some pizza for dinner. "One of us should go with him this time." Lloyd suggested. "We both know that he'll just ditch whoever goes with him." They stood in silence. A low buzzing interrupted their conversation. Lloyd pulled his phone out of his pocket, seeing the number.

"It's Nya." Lloyd announced before answering. "Hey Lloyd." The ninja of water's voice came over the phone. "Hi Nya. What's up?" Lloyd asked. "Well, our parents planned to have an outing tonight with me and Kai. But since Wu… you know, Kai has been acting strange around our father. I was hoping you could come and maybe help?" Of course she'd ask him. Lloyd knew what it was like to have an absent father suddenly return. Especially one who used to work for evil.

"Of course. Your parents cool with it?" Lloyd asked. "Yes. They said you could bring Misako if she'd like to join." Nya explained. "I'll be there. What time?" "6 tonight. We're going to meet a Chen's noodle place." Lloyd nodded, then realized Nya couldn't see him. "I'll meet you there." "Thanks Lloyd." With that, their conversation ended. "Nya just wanted to-" His words died on his tongue as he saw that the Earth Ninja wasn't in the room anymore. The items on the bed had also vanished. Shaking his head, Lloyd walked to Sensei Wu's room. Making sure no one was near, Lloyd slipped in.

It was still the same way Wu left it, except the small vault hidden behind the bookcase in the corner that contained the time blade. Otherwise, it was undisturbed. Lloyd walked over to where the cold candles Wu always lit when he meditated stood. Checking again to ensure no one was following, Lloyd pulled out a match and lit two lone candles before sitting in the floor. "I know you're not dead uncle, but it still feels as if you're gone." The green ninja whispered. "Everything has been different. We still go out to stop the bad guys every now and then, but they seemed to be all hiding and licking their wounds." Lloyd sighed. "Dad, Kai seems to be taking this kind of hard. I guess I can kind of thank you for giving me the knowledge to try and help." He chuckled a bit at the last answer.

"I wish the team could… come together again, like it was before. It almost seems like a repeat of what happened after Zane left. I don't want us to split up again." Lloyd sat in silence, staring at the candles as if they could respond. After more than ten minutes have passed though, he sighed in defeat. "Here I am, talking to candles." He muttered, cupping his head in his hands. A slight breeze blew, tickling his ears. A slight twinkling seemed to whisper to him, causing Lloyd to look up. The candles had blown out, but at their base, a small crystal sat. Lloyd, naturally curious, reached to pick up this sparkle-shaped crystal; but just as he touched it, it flashed brightly, burning the shape into his memory, and disappeared.

"Lloyd, where are you?" Lloyd opened his eyes. He was laying on his bed, somehow… "Lloyd! Dinner's ready!" The green ninja looked up to see the ninja of lightning standing in his doorway. The blue ninja's hair was messed up, as if he had been wrestling with something. "Oh, sorry Jay. I was taking a quick nap before dinner. What happened with you?" Jay looked confused, then remembered how messed up his hair was. "Oh! Hehe, I was trying to make a robot cat but it kind of backfired... literally." Lloyd suppressed a smile. Classic Jay, making a joke out of anything. "Zane just wanted me to call you for dinner." Lloyd nodded. "Ok, I'll be there." Jay nodded, then left.

Lloyd sighed, scratching his head. Was that all a dream? The Sensei-in-training headed towards the dining room. Everyone was already situated around the table as they hungrily waited for whatever tasty treat Zane had made. It was probably nothing. So the green ninja pushed the thought to the back of his mind.

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After dinner, a certain ninja in white was cleaning the kitchen. Lloyd, Kai, and Nya had left shortly after dinner, promising to return around eight. 'It's good Kai is getting out again. He needs a break.' Zane pondered his fiery friend, absent mindedly cleaning the kitchen. "Zane, look out!" Pixal's warning came, Zane freezing. He was about to start cleaning the toaster with a wet rag, and it was still plugged in. "Thank you for the warning Pixel." Zane replied, putting the rag away. "You seem to be more distracted lately." The robot voice commented. The nindroid didn't respond.

"Perhaps some fresh air will clear my mind." Zane stated after more then a few moments of quiet had passed, quickly heading outside. The grounds surrounding the airjitzu temple was quite lovely now that the flowers he'd planted with Misako had bloomed. A white butterfly caught his attention. "Pixel, do you recognize the species of that butterfly?" The titanium ninja asked. "What butterfly Zane? There's nothing there." Pixel asked, worried. The words seemed awfully familiar.

Too familiar.

Suddenly Zane was transported to the island where he was held captive as his friends fought in the tournament of elements. Except this time, there was no dragon. Instead, seven forms laid curled up on the ground, watched by something in the shadows. "Welcome Zane Julien."

 **End of Chapter One.**

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 **I hope you liked it and will return next chapter. Who are the eight figures? Who is in the shadows? Why is Zane there? Leave your thoughts in the review box and we'll see if you're right next chapter! Ta ta for now.**


	2. Chapter 2: Dream Walker

**_Chapter Two: Dream Walker_**

 **Hi readers! Another update! Sorry it took so long, school is throwing essay after essay at me and I didn't have time to write. Thanks for the reviews!**

 **Disclaimer: I do not own ninjago or mlp.**

* * *

 ** _Previously:_**

 _Suddenly Zane was transported to the island where he was held captive as his friends fought in the tournament of elements. Except this time, there was no dragon. Instead, seven forms laid curled up on the ground, watched by something in the shadows. "Welcome Zane Julien."_

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 ** _Chapter 2:_**

Zane looked up, focusing on the figure in the shadows. He sensed a strong aura coming from her, for indeed the voice sounded female, and didn't want to start any unnecessary confrontations from not paying attention. "Don't be alarmed. I do not come to give thee harm." She spoke regally, as if she were a ruler. "How do you know my name?" The nindroid question. It wasn't surprising that she knew his first name, as most citizens do. But only his father and the other ninja knew his last name.

"Because I forsaw your visit in a vision." The figure replied.

"Who are you?"

Silence greeted him, as if she was debating how to respond. After several painfully long heartbeats, she moved.

Her hair seemed to be made of night itself, and it flowed although there was no wind. The same went for her tail. Wait. Tail? "You are a horse?" He was a bit startled. "I am a pony. Alicorn to be more precise. I am Princess Luna, guardian of the night and dream realm, and one of the rulers of Equestria." Zane couldn't help but bow, her aura speaking of power that backed her words. She nodded in aproval.

"And who are they?" The ninja of Ice questioned, nodding to the figures that lay in the clearing. "You tell me." It wasn't as if she didn't know, but as if she knew that he already knew them. Curious and confused, Zane went closer to the red one with a brown mane. The style seemed as if Kai had given the pony his hair.

The blue one oddly resembled Jay as well. In fact, all five of the younger-looking ponies shared a resemblance with each of his friends, save for the fact they were ponies. Then Zane approached the white one.

It was snow white, and it had two wings folded against its side. Its mane had a familiar shape to it: how it was a bright blond and stuck straight up. And Zane felt drawn toward it, like a lost spirit to the place they had died. Thats when he realized, these ponies didn't just look like his friends; they _were_ the ninja in pony form. Armed with that knowledge, Zane turned to the elderly cream colored pony in the center.

He had a straw hat on, covering his eyes. However, Zane could see a long white beard that matched his white tail. A bamboo stick layed in the soil next to him.

"Wu..."

Indeed it was the missing sensei, not five feet away. But as he went to move closer, Luna stopped him. "Not yet."

"Why did you show me this?" The nindroid asked, trying to work out what he was seeing. "I only guided you."

"Then guide me to the answer."

"Zane Julian, remember what you have seen. I know not what your future holds. But your path is-" She had begun fading, consumed with darkness. Now, she was gone, as well as his surroundings.

He was alone in the dark, except for the seven ponies who were asleep. " ** _Yesss. Powerful_**. ** _They'll ssserve me well."_** Zane saw it. A dark mass that was even darker against the blackness of this space. It was heading straight for the seven ponies.

Straight for his friends.

Zane stood (when had he sat down?), his legs suddenly feeling weak. _'Just a little forwards.'_ The darkness was sucking his power source away, his light. " ** _What isss thisss?"_** The beast asked, as Zane stepped between him and the ponies. "Stay back." **_"Foolisshh mortal!"_** It dove at him with a screech that sparked a headache. Zane held up his arm and braced, before everything turned white.

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 **Sorry for the short chapter. Got busy writing essays for school. Who is this strange beast, and what did this mean? Find out next time, same fan story, same ninja channel. Frost out!**


	3. Chapter 3: Mending Bonds & Meeting Beast

**Hello ninja readers! I have returned again with another chapter! I know the story has been kind of slow so far, but it picks up soon... hopefully.** **Any how, here's the next chapter, and Kai finally makes his appearance.**

 **Btw, this takes place about six months after S7, meaning it's 6 months before season 8. I'm taking into account how the characters changed during that year period between, but not everything js gonna fit with canon.**

 **Disclaimer: I only own story ideas. Read and Review!**

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 **Chapter Three: Mending bonds and Meeting Beasts**

 _Kai shifted in his seat next to his father._ Ray, the older master of Fire, was scanning the map in his hands. "What do you want to do first son?" _Son._ It sounded strange to be called son. The one thing he's never been called since infantry. "I don't know… dad." That felt strange too.

Maya and Misako were eagerly discussing stories from when the ninja were younger, much to Lloyd's embarrassment. It was quite amusing. The green ninja, the protector of Ninjago, beet red at the mention of the green blanket that he had clung onto so tightly and called "Gwee" (probably meaning green, but the kid had apparently forgotten the last "n". Lloyd looked right at Kai, and took a double take at the grin on the red ninja's face. A _real_ grin. And though it was small, it was the first one in six months to grace the master of fire's face.

His thoughts were disturbed by the cry of joy that Ray let out as he saw the ferris wheel open. Just like Wu had done all those years ago. _Wu was like a father to me… but now he's gone and my real father is back._ Lloyd approached him. "Hey Kai, why don't you and your dad go to the ferris wheel? I'll hold onto those bags for you." Right, the three bags filled with miscellaneous prizes they'd won.

"Alright."

So father and son went to the ferris wheel, and they got on. They sat in silence for a bit, until Ray broke the tension. "I'm sorry." Kai blinked, confused as to why his father was apologizing . "I left you and Nya alone, while I didn't try to escape... " Kai rested a hand on Ray's shoulder. "It's okay. I forgave you when we rescued you and mom from the time twins."

Ray grinned. "Wu trained you well. I couldn't be more proud of how you've grown." Kai smiled sadly. "Wu… He was like another father. And for a moment, I had two. Now he's gone." A small tear threatened to make itself known. "I know Kai. But we will find him. Time won't keep family apart forever."

Once the group returned home, they were greeted by a blue blur running up. It was Jay, but worryand concerned was etched onto his face. "Jay, what's wrong?" Kai asked, growing concerned as well.

"It's Zane! I came outside to check on him, only to see that he was unconscious on the ground, over by those bushes. It looks like he got his with something hard because there's a big crack on his forehead." Lloyd hurriedly explained, pulling the ninja inside.

"But what caused it?" Lloyd asked, wondering what was strong enough to attack and injure Zane.

"I don't know." Jay explained. Nya rushed past, as she had the most medical knowledge out of the group, especially when it came to the specific needs they each had. Needs like how Kai's temperature dropped dangerously low when he was sick and needed to be kept warm, and how Jay consumed a lot of calories when injured because of his quick healing (must have something to do with the quick nature of lightning). "Nya's on it, he'll be okay Jay." Cole said, and Jay nodded, trusting the Earth master.

Their conversation was cut short as they heard a scream. "Nya!" Kai took off to find his sister, Jay almost beating him out the door. Cole and Lloyd were in pursuit as well, but a low hissing was heard that caused them to freeze. Lloyd grabbed a sword off the wall, tossing the other to Cole. **_"Foolisshhh sssstrangersss. Thisss isssn't your fight!"_** It seemed to echo from every corner. "It is now! If you've harmed any of my friends-" A sudden movement out of the corner of his vision was the only warning before something collided with his side.

"Lloyd!"

Lloyd rolled with it, years of training kicking in. Instead of colliding with the opposite wall, he managed to bounce off it and strike at the shadow with his blade. It hissed in annoyance or pain. **_"Sssso annoying. Alwaysss protecting each other."_** Oh, so it was the former. The shadowy figure collected together into a mass, but it was unrecognizable save for the deathly white eyes. **_"I'll have to fix that…"_** And he lunged. Lloyd raised his blade to fight back, but at the last minute the figure went after Cole, who couldn't block in time.

Lloyd sent an energy bubble to protect his brother. The green energy, once it touched the shadow, burst into green flames. They shadow screamed. "Lloyd, how are you doing that?" Lloyd just stood in shock. The shadow grew larger, growling. **_"You're too powerful together… but there are wayssss to break you apart!"_** Then it dove at the lights, drowning the room into darkness.

Lloyd was about to fight, when sleep tugged at his mind. "No, its part of its trick!" He muttered, trying to fight off the mental attack. He closed his eyes, only to wake up in a forest. "Hello?" He called out, his voice echoing. There was no reply, save for the sing song voice of the wind barely louder than a whisper and almost drowned out by the ringing in his ear. After it repeated several times, Lloyd started making out the words.

 _"Lloyd Garmadon, Ninja Green._

 _Must protect a world unseen._

 _From foes breath does danger reek,_

 _The family chosen must he seek._

 _A trusting Flame near Ocean that lends a hand ._

 _The joking Lightning above the sturdy Land ._

 _Friendly Ice with the Energy within,_

 _Unite them all, the war to win._

 _Lloyd Garmadon, ninja no more._

 _The days turned back, different then before._

 _Remember, learn, dream, unlock._

 _Turn back time, fix the clock. "_

That was the song that Lloyd heard before sleep finally overcame him.

 _Then there was nothing._

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 **Ooo, I wonder how the beast is going to "fix this"? Leave your theories in the comments. Who knows, maybe you're right. My question for this chapter is who is your favorite ninjago villain? Maybe they might cameo later on... Adios. Hasta luego!**


	4. Chapter 4: To Where and Back Again

Greetings friends! Its been awhile, eh? Thank you for your patience, and it shall be rewarded with this chapter! Thanks again!

Disclaimer: I do not own ninjago or my little pony.

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 ** _Previously on MLP:MOH-_**

 _That was the song that Lloyd heard before sleep finally overcame him._

 _Then there was nothing._

 **Chapter 4: To Where and Back again**

A purple alicorn paced back and forth, her horn aglow with magic. This magic was holding a book, a very old and dusty book. Off to the side, clearly not amused, was a baby dragon. His eyes followed the path of the pony, wondering what sent his friend into such a tizzy. "What's wrong Twilight?" He questioned.

The pony, Twilight, paused her pacing for a moment. "I'm getting reports of some strange shadow that was terrorizing ponies in Appleloosa." She stated, looking at the paper again. "What's the problem? We've dealt with things like this before." The dragon replied, relaxing. They had faced many monsters before. This one will be a piece of cake. "The thing is, Spike, there's also been reports of strange fluxuations of magic in Canterlot, the Crystal Empire, and Cloudsdale! Followed by the same dark shadow!" So it was more spread out than they originally thought. That would make things harder. Before the dragon could reply, the door was thrown open and an orange pony sporting a cowboy hat and a blue pegasus with a rainbow mane bursted in.

"Twilight, you've gotta see this."

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Zane felt cold, which was odd since… _Since what?_ Zane was confused, wondering why he had thought he shouldn't feel cold. Something was moving nearby, and he wanted to know what it was. He opened his eyes to see a yellow... unicorn? But unicorns didn't exist. _No, they did. He once worked for one. Why was his mind arguing with itself?_ Zane shook his head, chasing the discording thoughts away. "Hey, he's awake!" The yellow unicorn exclaimed. "Hush Daisy. He seems to be frightened." Another voice, coming from a pink alicorn, said. Zane felt as if he should know who she was, but it wasn't there.

"Do you know where your parents are?" The pink one asked. Zane racked his brain, trying to think of what should have been easy to recall. He reached for a name, a face, a location or _anything_ to tie him to a home. Alas, his searches came up empty. He shook his head. "No madam. I don't remember where they are. I don't know who they are." His voice was flat and almost monotonous, lined with sadness for something he lost that he never knew. However the oddity of it wasn't what scared him. It was the fact that is was foreign to him. Surely he must be able to recognize his own voice! The pink alicorn sighed sadly. "I'm sorry little one. Why don't we bring you to Miss Orchid's until we can locate them?" She said gently. Zane nodded, trying to stand but falling on his face.

The yellow unicorn, Daisy, giggled. "You walk on all four hooves silly!" _Four hooves_? Zane looked down to see he indeed had four white-furred hooves. _But hadn't he always had them? Why did they seem so strange to him now? And why did his head hurt?_ Standing, this time balancing on all four hooves and not just the back two. Tired, he followed the two ponies towards wherever they were going. _Why can't I remember?_

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Lloyd hated bunnies. Okay, not all of them. But this bunny was mean! All he wanted to do was sleep, and this bunny kept hitting him with its foot and squeaking at him. If his dad was here then he'd just push the bunny away and force it to leave him alone. _But where was his dad?_ He woke up in this cottage, with a yellow pegasus making soup. How dare she make soup? Lloyd Garmadon wanted ice cream! "Leave me alone, bunny, or I'll unleash the might of the Serpentine on you!" Lloyd exclaimed, trying to sound tough. He had to be tough, because if he wasn't then they would take advantage and pick on him. The son of Garmadon shouldn't be treated that way! And would this bunny just go away?

"Who's the Serpentine?" The pegasus asked, breaking his inner monologue. Lloyd was shocked at her lack of knowledge, but he was much smarter than her anyway. "They're…" Lloyd started to answer, then fell silent as the answer didn't come. _Where had that name came from?_ He felt as if something was missing, that something was wrong here with this scene. Of course, it was that he was entertaining the pegasus and not eating candy or ice cream. That had to be it.

"I don't have to tell you!" He growled, turning away to hide his embarrassment of being unable to answer. She was trying to be nice, but he knew it was a lie. A trick to get him to lower his guard, and when he did she would be mean and taunt him. Besides, he didn't need anybody. They'd leave anyway, like his mother did. And his father… _where was he anyway?_ Probably left to get ice cream. But, wasn't there a point where he wasn't alone? Wasn't there someone who was like his older brother? No, he was always alone. It must have been a pointless dream. No, he didn't need _anyone_.

 _Lloyd Garmadon didn't need anypony_. And with that inner declaration, he felt something in him slip away. But he didn't care.

* * *

Cole hated the dark mines. Don't get him wrong, he loved the cool feeling of the sturdy earth beneath his hooves, and the way it shaped his world, but he didn't enjoy being held miles beneath the surface, mining at the heart of the land. "Don't dawdle!" The large stallion grunted, pushing him forwards. The stallion, who hadn't given a name except to be called Sir, was large. His pelt was once an indigo color but now was covered with a fine layer of dust that settled from the ceiling, with one crippled wing hanging uselessly against his side, and the other used to hold a cold drink he refused to share.

Cole had woken up somewhere near the outskirts of a town called Appleoosa, a small country town that smelled of honey apples and fun. It was calming to him, who had not a clue how he got there or why his memories had left him. Not long after, however, he was brutally thrown back onto a large rock that left him dazed and confused. He was hogtied, gagged, and thrown into a covered wagon with several other young colts. They were taken to an abandoned mine, long forgotten by the ponies who lived in Appleoosa, and then forced to work. Mining for the jewels of the earth that fetched a hefty price in the markets up north where it was too cold to mine and in Cloudsdale, where there was no rock to mine with. No one knew they were there, there was no one to miss them for they were all either orphans or runaways.

Cole glared at the stallion in charged underneath his black mane. ' _If only I had my… my what?'_ What was it he was missing? It must be important, as without it he felt empty. _'Whatever it is, I will find it. But first, we need to get out of here.'_

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 **That's all for this chapter! So now we know what happened to three of our group of ninja, but what about the other three? Where has their memories gone? And last but not least, what will they do now? It's a mystery for the next chapter. Feel free to comment ideas!**

 **Today's question is: Who is your favorite elemental master?**

 **Thanks for reading!**


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